Study of structural relationship between human ribosomal proteins P1 and P2.

• Other Authors: Chiu, Yu Hin Teddy.
• Format: Others
• Language: English; Chinese
• Published: 2008
• Subjects: Ribosomes > Structure; Ribosomal Proteins > ultrastructure
• Online Access: http://library.cuhk.edu.hk/record=b5893521; http://repository.lib.cuhk.edu.hk/en/item/cuhk-326279

Chiu, Yu Hin Teddy. === Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. === Includes bibliographical references (leaves 118-129). === Abstracts in English and Chinese. === Acknowledgements --- p.i === Abstract --- p.ii === Table of Content --- p.vi === Abbreviations --- p.x === Naming system for mutant proteins --- p.xi === Abbreviation for amino acid --- p.xii === Chapter Chapter 1 --- Introduction --- p.1 === Chapter 1.1 --- What are acidic ribosomal proteins? --- p.1 === Chapter 1.2 --- Why P-proteins are so important? --- p.13 === Chapter 1.3 --- Research objectives --- p.15 === Chapter Chapter 2 --- Materials and Methods --- p.17 === Chapter 2.1 --- List of buffers and media --- p.17 === Chapter 2.1.1 --- Preparation of buffers and media --- p.17 === Chapter 2.1.2 --- Buffers for preparing competent cells --- p.17 === Chapter 2.1.3 --- Media for bacterial culture --- p.17 === Chapter 2.1.4 --- Buffers for nucleic acid electrophoresis --- p.19 === Chapter 2.1.5 --- Buffers for protein electrophoresis --- p.19 === Chapter 2.1.6 --- Buffers for interaction studies using BIAcore 3000 --- p.21 === Chapter 2.2 --- General methods --- p.23 === Chapter 2.2.1 --- Preparation of Escherichia coli (E.coli.) competent cells --- p.23 === Chapter 2.2.2 --- Transformation of Escherichia coli (E.coli.) competent cells --- p.23 === Chapter 2.2.3 --- DNA cloning --- p.24 === Chapter 2.2.3.1 --- DNA cloning by polymerase chain reaction (PCR) --- p.24 === Chapter 2.2.3.2 --- Agarose gel electrophoresis of DNA --- p.25 === Chapter 2.2.3.3 --- Extraction and purification of DNA from agarose gels --- p.25 === Chapter 2.2.3.4 --- Restriction digestion of DNA --- p.25 === Chapter 2.2.3.5 --- Ligation of digested insert and expression vector --- p.27 === Chapter 2.2.3.6 --- Verification of insert by PCR --- p.27 === Chapter 2.2.3.7 --- Mini-preparation of plasmid DNA --- p.28 === Chapter 2.2.4 --- Polyacrylamide gel electrophoresis (PAGE) of protein --- p.29 === Chapter 2.2.4.1 --- SDS-polyacrylamide gel electrophoresis (SDS-PAGE) --- p.29 === Chapter 2.2.4.2 --- Tricine SDS-polyacrylamide gel electrophoresis --- p.30 === Chapter 2.2.4.3 --- Native polyacrylamide gel electrophoresis --- p.31 === Chapter 2.2.4.4 --- Commassie brilliant blue staining of proteinin polyacrylamide gel --- p.32 === Chapter 2.2.4.5 --- Zinc Imidazole staining of protein in polyacrylamide gel --- p.33 === Chapter 2.2.5 --- Protein concentration determination --- p.33 === Chapter 2.2.6 --- Expression of recombinant proteins --- p.33 === Chapter 2.2.6.1 --- Expression of recombinant proteins using LB --- p.33 === Chapter 2.2.6.2 --- Expression of recombinant proteins using minimal medium --- p.34 === Chapter 2.2.6.3 --- Harvest and lysis of bacterial cell culture --- p.34 === Chapter 2.3 --- Protein purification --- p.36 === Chapter 2.3.1 --- Purification of ribosomal protein P1 and its deletion mutants --- p.36 === Chapter 2.3.1.1 --- Purification of P1 --- p.36 === Chapter 2.3.1.2 --- Purification of P1ΔC25 --- p.36 === Chapter 2.3.1.3 --- Purification of HisMBP-P1ΔC40 and HisMBP-P1ΔC47 --- p.37 === Chapter 2.3.2 --- Purification of ribosomal protein P2 and its deletion mutants --- p.38 === Chapter 2.3.2.1 --- Purification of P2 --- p.38 === Chapter 2.3.2.2 --- Purification of P2ΔC46 and P2ΔC55 --- p.39 === Chapter 2.4 --- "Preparation and purification of protein complexes formed by P1, P2 and their truncation mutants" --- p.40 === Chapter 2.4.1 --- Preparation of complexes by Co-refolding in urea buffer --- p.40 === Chapter 2.4.1.1 --- Preparation of P1 or P1ΔC25 involved complexes --- p.40 === Chapter 2.4.1.2 --- Preparation of P1ΔC40/ P2ΔC46 and P1ΔC47/ P2ΔC46 --- p.41 === Chapter 2.4.2 --- Preparation of complexes by direct mixing --- p.42 === Chapter 2.5 --- Laser light scattering for the determination of molecular weight of protein and their complexes --- p.43 === Chapter 2.5.1 --- Chromatography mode light scattering experiment (SEC/LS) --- p.43 === Chapter 2.6 --- Interaction study of P1 and P2 using BIAcore 3000 surface plasmon resonance (SPR) biosensor --- p.45 === Chapter 2.6.1 --- Immobilization of P2 onto CM5 sensor chips --- p.45 === Chapter 2.6.2 --- Kinetic measurements of P1 and P2 interaction --- p.46 === Chapter Chapter 3 --- Determination of domain boundaries for dimerization of P1/P2 --- p.46 === Chapter 3.1 --- Introduction --- p.48 === Chapter 3.2 --- Preparation of P1，P2 and their truncation mutants --- p.50 === Chapter 3.2.1 --- Construction of P1 and P2 N-terminal domains (NTDs) --- p.50 === Chapter 3.2.2 --- P1 and its truncation mutants were purified in denaturing condition --- p.53 === Chapter 3.2.3 --- "P2, P2AC46 and P2AC55 were purified" --- p.56 === Chapter 3.3 --- Formation of complexes from P1，P2 and their truncation mutants --- p.59 === Chapter 3.3.1 --- "P1, P2 and their truncation mutants interact to yield protein complexes" --- p.49 === Chapter 3.3.2 --- P1AC47/P2AC46 is the smallest N-terminal domain complex --- p.63 === Chapter 3.4 --- Perturbation of P2 NTD upon binding with P1 --- p.65 === Chapter 3.4.1 --- "1H, 15N 一 HSQC spectrum of P2AC46 changed significantly upon binding with P1" --- p.65 === Chapter 3.4.2 --- P1/P2AC46 prepared by co-refolding and direct mixing give the same HSQC spectra --- p.66 === Chapter 3.5 --- Discussion --- p.69 === Chapter Chapter 4 --- Stochiometry of P1/P2 Complex is revealed by Light scattering --- p.72 === Chapter 4.1 --- Introduction --- p.72 === Chapter 4.2 --- P1 and P2 interact in 1:1 molar ratio --- p.77 === Chapter 4.2.1 --- Purified P2 exists as homo-dimer in solution --- p.77 === Chapter 4.2.2 --- The stochiometry of P1/P2 complex is 1:1 --- p.78 === Chapter 4.3 --- Stochiometries of P1 and P2 truncation mutant complexes varied from the full-length counterparts --- p.81 === Chapter 4.3.1 --- P2AC46 and P2AC55 exist as homo-dimer in solution --- p.81 === Chapter 4.3.2 --- "P1/P2AC46, P1AC25/P2 and P1AC40/P2AC46 retain the hetero-dimeric stochiometry of 1:1" --- p.82 === Chapter 4.3.3 --- P2AC55 involved complexes show a different stochiometry --- p.83 === Chapter 4.4 --- Discussion --- p.87 === Chapter Chapter 5 --- Binding kinetics of P1/P2 complex studied by surface plasmon resonance --- p.92 === Chapter 5.1 --- Introduction --- p.92 === Chapter 5.2 --- Kinetic parameters of P1 and P2 interaction is revealed by surface plasmon resonance --- p.95 === Chapter 5.2.1 --- P2 was coupled to CM5 sensor chip surface for kinetic studies --- p.95 === Chapter 5.2.2 --- Reduction of basal response after the 1st binding of P1 --- p.96 === Chapter 5.2.3 --- P1 induced a great change in response unit than P2 upon binding with immobilized P2 --- p.99 === Chapter 5.2.4 --- Kinetic parameters of P1 and P2 interaction was studied by introducing P1 to the sensor chip surface --- p.101 === Chapter 5.2.5 --- Dissociation constant derived from 1:1 Langmuir binding isotherm --- p.102 === Chapter 5.2.6 --- Dissociation constant derived from responses at equilibrium (Req) --- p.103 === Chapter 5.3 --- Discussion --- p.106 === Chapter Chapter 6 --- Conclusion and discussion of the study --- p.112 === References --- p.118 === Appendix --- p.130